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Django app for syncing and storing human genome reference data

Project description

https://badge.fury.io/py/django-genome.svg https://travis-ci.org/chopdgd/django-genome.svg?branch=develop https://codecov.io/gh/chopdgd/django-genome/branch/develop/graph/badge.svg Updates Python 3

Django app for syncing and storing human genome reference data

Documentation

The full documentation is at https://django-genome.readthedocs.io.

Quickstart

Install Django Genome:

pip install django-genome

Add it to your INSTALLED_APPS (along with DRF and django-filters):

INSTALLED_APPS = (
    ...
    'rest_framework',
    'django_filters',
    ...
    'genome',
    ...
)

Add Django Genome’s URL patterns:

from genome import urls as genome_urls


urlpatterns = [
    ...
    url(r'^', include(genome_urls, namespace='genome')),
    ...
]

Initial sync for genome models:

python manage.py genome_sync

Features

  • Includes models for Genome, Chromosome, CytoBand, Gene, Transcript, and Exons
  • Syncs data for hg18, hg19, hg38 from HGNC and UCSC

Running Tests

Does the code actually work?

source <YOURVIRTUALENV>/bin/activate
(myenv) $ pip install tox
(myenv) $ tox

Credits

Tools used in rendering this package:

History

0.1.0 (2017-12-30)

  • First release on PyPI.
  • Initial models and REST API
  • Syncs data from HGNC and UCSC to build database

0.2.0 (2018-01-05)

0.2.0 Changelog

  • Improved REST API Filters
  • made Chromosomes and Gene Symbols save as uppercase to maintain consistency

0.2.1 (2018-01-08)

0.2.1 Changelog

  • Fixed issues with migrations

0.2.2 (2018-01-12)

0.2.2 Changelog

  • Fixed route names for SimpleRouter

0.3.0 (2018-02-09)

0.3.0 Changelog

  • Updated requirements to the latest

0.4.0 (2018-03-30)

0.4.0 Changelog

  • Added API for chromosomes
  • Changed gene_symbol from being unique

0.5.0 (2018-04-04)

0.5.0 Changelog

  • Added GraphQL Nodes

0.6.0 (2018-04-07)

0.6.0 Changelog

  • Added support for Django 2 and Python 3.6
  • Dropped support for Django < 1.11 and Python 2.7, 3.3, 3.4

0.6.1 (2018-04-18)

0.6.1 Changelog

  • Updated 3rd party libs

0.6.2 (2018-05-14)

0.6.2 Changelog

  • Updated chromosomes sync to ensure lexicographic ordering of chromosomes

0.6.3 (2018-05-16)

0.6.3 Changelog

  • Updated sync to be able to skip sync of exons

0.6.4 (2018-05-16)

0.6.4 Changelog

  • Updated setup.py to read requirements.txt

0.7.0 (2018-06-01)

0.7.0 Changelog

  • Added Gene List model
  • Removed support for GraphQL - this is not needed here. Applications that import this package can set up Nodes/Schema using models

0.7.1 (2018-06-07)

0.7.1 Changelog

  • #54 - Updated management methods to allow for updating when retrieving latest changes from RefSeq
  • #56 - Updated Gene model to have property ensembl_gene_id - which will check HGNC and Ensembl provided gene Ids

0.7.2 (2018-08-13)

0.7.2 Changelog

  • Updated 3rd party requirements. Some requirements had changed so it was causing failures

0.7.3 (2018-09-26)

0.7.3 Changelog

  • Updated transcript model to include preferred transcript boolean

0.7.4 (2018-10-29)

0.7.4 Changelog

  • Updated 3rd party libs

0.7.6 (2018-11-27)

0.7.6 Changelog

  • HGNC changed their headers - so gene sync was broken. Made reading headers case insensitive

0.7.7 (2019-02-08)

0.7.7 Changelog

  • Updated 3rd party libs
  • Updated tests to use py.test fixtures correctly

0.7.8 (2019-04-10)

0.7.8 Changelog

  • Updated 3rd party libs
  • Updated travis to use xenial distribution. Django 2.1 dropped support for SQLite < 3.8.3

0.8.0 (2019-05-31)

0.8.0 Changelog

  • Refactored sync to use UCSC MySQL database connection
  • Updated sync to incorporate transcript refseq versions
  • Updated package to use latest cookiecutter template

0.8.1 (2019-06-14)

0.8.1 Changelog

  • Gene entries created from RefSeq where not setting the chromosome attribute
  • Added better logging functionality

0.8.2 (2019-07-26)

0.8.2 Changelog

  • Updated 3rd party libs

0.9.0 (2019-08-02)

0.9.0 Changelog

  • Updated Gene data model and sync to include date approved/modified.

0.9.1 (2019-08-05)

0.9.1 Changelog

  • Fixed issue with bundle not being published correctly

0.9.2 (2019-08-09)

0.9.2 Changelog

  • Updated 3rd party libs

0.9.3 (2019-09-09)

0.9.3 Changelog

  • Updated 3rd party libs

1.0.0 (2019-11-01)

1.0.0 Changelog

  • Updated Gene model to make sure it is unique on symbol
  • First, production release

1.1.0 (2019-11-26)

1.1.0 Changelog

  • Updated dependencies

1.1.1 (2020-03-12)

1.1.1 Changelog

  • #149 - Updated the genome sync to deal with new headers
  • #144 - preferred transcript sync will now use version numbers

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